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#!/usr/bin/env python |
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# -*- coding: utf-8 -*- |
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""" |
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/home/magnus/rna-evo-malibu/ade # run here not up |
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""" |
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from __future__ import print_function |
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import argparse |
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import os |
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import glob |
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View Code Duplication |
def get_parser(): |
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parser = argparse.ArgumentParser( |
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description=__doc__, formatter_class=argparse.RawDescriptionHelpFormatter) |
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parser.add_argument('-d', "--dryrun", |
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action="store_true", help="dry run", default=False) |
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parser.add_argument('-p', '--path', help="", default='') |
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parser.add_argument('-c', '--case', help="only one case, for test") |
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parser.add_argument('-e', '--exe', help="only one case, for test") |
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parser.add_argument("-v", "--verbose", |
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action="store_true", help="be verbose") |
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return parser |
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def exe(cmd, dryrun=False): |
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print(cmd) |
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if not dryrun: os.system(cmd) |
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if __name__ == '__main__': |
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parser = get_parser() |
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args = parser.parse_args() |
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if args.path: |
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os.chdir(args.path) |
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root = os.getcwd() |
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cases = glob.glob('*') |
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for c in cases: |
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# print('Case: ', c) |
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# mode only for a specific case |
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os.chdir(root) # change to run and go to another case |
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if args.case: # only if this is used |
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if c != args.case: |
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if args.verbose: print('!!! skip ' + c + '!!!') |
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continue |
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# if not break ed, use this |
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if os.path.isdir(c): |
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print ('Inside %s' % c) |
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os.chdir(c) # go inside a folder |
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if args.exe: |
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exe(args.exe) |
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#subcases = glob.glob('*.fa') |
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#for sc in subcases: |
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## for i in [1000]: # |
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## exe('rm *min.out.*.pdb', dryrun) |
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## exe('mkdir %s_top%i' % (c, i), dryrun) |
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## exe('extract_lowscore_decoys.py *min.out %i' % (i), dryrun) |
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## exe('mv -v *min.out.*.pdb %s_top%i' % (c, i), dryrun) |
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## os.chdir(root) |
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malibu_folder = c.replace('_cst', 'cst').replace('farna_', '') |
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print(c, malibu_folder) |
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# exe('trash top100') |
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exe('mkdir top100') |
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exe('pwd') |
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os.chdir('top100') # cd top100 didn't work ?! |
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exe('rsync -v malibu:"~/rna-evo-malibu/_rp13_Stanford/_reg_vs_cst/%s/*.pdb" . ' % malibu_folder) |
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exe('rm c.*pdb') |
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exe('rm *out.1[0-9][1-9]*.pdb') |
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exe('rm *out.1[1-9]0*.pdb') |
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exe('rm *out.200.pdb') |
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exe('rm p[0-9].pdb') |
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exe('rna_pdb_toolsx.py --rpr --renumber_residues --inplace *') |
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os.chdir('..') |
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exe('evox.py -c rp13') |
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mmagnus /
rna-tools
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